Comprehensive Analysis of Full-Length Transcriptome Profiling, Genetic and Phenotypic Variation in Multiplier Onion (Allium cepa var. aggregatum) Accessions in China

Multiplier onion (Allium cepa L. var. aggregatum) is an important bulbous vegetable widely utilized for culinary, condimental, and medicinal purposes. However, limited research on its genetic diversity and phenotypic variation has hindered the development and utilization of superior cultivars. In this study, we conducted full-length transcriptome profiling to obtain unique transcripts and develop large-scale simple sequence repeat (SSR) markers. Subsequently, we employed integrative analysis to characterize the genetic and phenotypic variation of 263 multiplier onion accessions in China. Full-length transcriptome sequencing utilizing PacBio technology generated 61,108 high-quality non-redundant transcripts with an average length of 1816 bp, from which we developed 4124 SSR markers encompassing 100 motif types. Population structure, principal component analysis, and neighbor-joining phylogenetic analysis classified the 263 multiplier onion accessions into two distinct subpopulations: Pop1, consisting of 236 accessions primarily from Heilongjiang Province, and Pop2, comprising 27 accessions mostly from Shaanxi Province. Phenotypic evaluation demonstrated significant variation in bulb traits, with single bulb weight (SBW) exhibiting the highest variability (0.75–29.94 g; CV = 70.10%), followed by total bulb weight per plant (BW) (5.00–168.83 g; CV = 58.34%), indicating considerable potential for breeding high-yield varieties. Correlation analysis indicated that the SBW and BW had significantly positive correlations with multiple traits, including bulb height, bulb transverse diameter, diameter of basal plate of bulb, diameter of bulb neck, and number of cloves per bulb. Our findings provide a valuable genetic and phenotypic resource for the conservation and utilization of multiplier onion germplasms.